# Name of your program
package "RNAaliduplex" # don't use package if you're using automake
purpose "Predict conserved RNA-RNA interactions between two alignments"
usage "RNAaliduplex [options] <file1.aln> <file2.aln>"

# Version of your program
#version "2.0"   # don't use version if you're using automake


# command line options passed to gengetopt
args "--file-name=RNAaliduplex_cmdl --include-getopt --default-optional --unamed-opts --func-name=RNAaliduplex_cmdline_parser --arg-struct-name=RNAaliduplex_args_info"


description "The program reads two alignments of RNA sequences in CLUSTAL format and predicts optimal and\
 suboptimal binding sites, hybridization energies and the corresponding structures. The calculation\
 takes only inter-molecular base pairs into account, for the general case use RNAcofold. The use of\
 alignments allows to focus on binding sites that are evolutionary conserved. Note, that the two\
 input alignments need to have equal number of sequences and the same order, i.e. the 1st sequence\
 in file1 will be hybridized to the 1st in file2 etc.\n\nThe computed binding sites, energies, and\
 structures are written to stdout, one structure per line. Each line consist of: The structure in\
 dot bracket format with a \"&\" separating the two strands. The range of the structure in the two\
 sequences in the format  \"from,to : from,to\"; the energy of duplex structure in kcal/mol.\nThe\
 format is especially useful for computing the hybrid structure between a small probe sequence and\
 a long target sequence.\n\n"

# Options
section "General Options"
sectiondesc="Below are command line options which alter the general behavior of this program\n"

option  "deltaEnergy" e
"Compute suboptimal structures with energy in a certain range of the optimum (kcal/mol).\
 Default is calculation of mfe structure only.\n\n"
float
typestr="range"
optional

option  "sorted"  s
"print output sorted by free energy\n\n"
flag
off

section "Model Details"

option  "temp"  T
"Rescale energy parameters to a temperature of temp C. Default is 37C.\n\n"
double

option  "noTetra" 4
"Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.\n\n"
flag
off

option  "dangles" d
"How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops\n"
details="\nWith -d1 only unpaired bases can participate in at most one dangling end, this is the\
 default for mfe folding but unsupported for the partition function folding.\n\nWith -d2 this check is ignored,\
 dangling energies will be added for the bases adjacent to a helix on both sides in any case; this is the\
 default for partition function folding (-p).\nThe option -d0 ignores dangling ends altogether (mostly for\
 debugging).\nWith -d3 mfe folding will allow coaxial stacking of adjacent helices in multi-loops. At the\
 moment the implementation will not allow coaxial stacking of the two interior pairs in a loop of degree 3\
 and works only for mfe folding.\n\nNote that by default (as well as with -d1 and -d3) pf and mfe folding\
 treat dangling ends differently. Use -d2 in addition to -p to ensure that both algorithms use the same\
 energy model.\n\n"
int
default="2"
optional

option  "noLP"  -
"Produce structures without lonely pairs (helices of length 1).\n"
details="For partition function folding this only disallows pairs that can only occur isolated. Other\
 pairs may still occasionally occur as helices of length 1.\n\n"
flag
off

option  "noGU"  -
"Do not allow GU pairs\n\n"
flag
off

option  "noClosingGU" -
"Do not allow GU pairs at the end of helices\n\n"
flag
off

option  "noconv"  -
"Do not automatically substitude nucleotide \"T\" with \"U\"\n\n"
flag
off

option  "nsp" -
"Allow other pairs in addition to the usual AU,GC,and GU pairs.\n"
details="Its argument is a comma separated list of additionally allowed pairs. If the\
 first character is a \"-\" then AB will imply that AB and BA are allowed pairs.\ne.g.\
 RNAfold -nsp -GA  will allow GA and AG pairs. Nonstandard pairs are given 0 stacking\
 energy.\n\n"
string
optional

option  "paramFile" P
"Read energy parameters from paramfile, instead of using the default parameter set.\n"
details="A sample parameter file should accompany your distribution.\nSee the RNAlib\
 documentation for details on the file format.\n\n"
string
typestr="paramfile"
optional

text    "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\
 rna@tbi.univie.ac.at\n"